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    Surface moisture and vegetation cover analysis for drought monitoring in the southern Kruger National Park using Sentinel-1, Sentinel-2, and Landsat-8
    (MDPI, 2018-09) Urban, M.; Berger, C.; Mudau, T.E.; Heckel, K.; Truckenbrodt, J.; Odipo, V.O.; Smit, I.P.J.
    During the southern summer season of 2015 and 2016, South Africa experienced one of the most severe meteorological droughts since the start of climate recording, due to an exceptionally strong El Niño event. To investigate spatiotemporal dynamics of surface moisture and vegetation structure, data from ESA's Copernicus Sentinel-1/-2 and NASA's Landsat-8 for the period between March 2015 and November 2017were utilized. In combination, these radar and optical satellite systems provide promising data with high spatial and temporal resolution. Sentinel-1 C-band data was exploited to derive surface moisture based on a hyper-temporal co-polarized (vertical-vertical-VV) radar backscatter change detection approach, describing dynamics between dry and wet seasons. Vegetation information from a TLS (Terrestrial Laser Scanner)-derived canopy height model (CHM), as well as the normalized difference vegetation index (NDVI) from Sentinel-2 and Landsat-8, were utilized to analyze vegetation structure types and dynamics with respect to the surface moisture index (SurfMI). Our results indicate that our combined radar-optical approach allows for a separation and retrieval of surface moisture conditions suitable for drought monitoring. Moreover, we conclude that it is crucial for the development of a drought monitoring system for savanna ecosystems to integrate land cover and vegetation information for analyzing surface moisture dynamics derived from Earth observation time series.
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    A metagenomic viral discovery approach identifies potential zoonotic and novel mammalian viruses in Neoromicia bats within South Africa
    (Public Library of Science, 2018-03) Geldenhuys, M.; Mortlock, M.; Weyer, J.; Bezuidt, O.; Seamark, E.C.J; Kearney, T.
    Species within the Neoromicia bat genus are abundant and widely distributed in Africa. It is common for these insectivorous bats to roost in anthropogenic structures in urban regions. Additionally, Neoromicia capensis have previously been identified as potential hosts for Middle East respiratory syndrome (MERS)-related coronaviruses. This study aimed to ascertain the gastrointestinal virome of these bats, as viruses excreted in fecal material or which may be replicating in rectal or intestinal tissues have the greatest opportunities of coming into contact with other hosts. Samples were collected in five regions of South Africa over eight years. Initial virome composition was determined by viral metagenomic sequencing by pooling samples and enriching for viral particles. Libraries were sequenced on the Illumina MiSeq and NextSeq500 platforms, producing a combined 37 million reads. Bioinformatics analysis of the high throughput sequencing data detected the full genome of a novel species of the Circoviridae family, and also identified sequence data from the Adenoviridae, Coronaviridae, Herpesviridae, Parvoviridae, Papillomaviridae, Phenuiviridae, and Picornaviridae families. Metagenomic sequencing data was insufficient to determine the viral diversity of certain families due to the fragmented coverage of genomes and lack of suitable sequencing depth, as some viruses were detected from the analysis of reads-data only. Follow up conventional PCR assays targeting conserved gene regions for the Adenoviridae, Coronaviridae, and Herpesviridae families were used to confirm metagenomic data and generate additional sequences to determine genetic diversity. The complete coding genome of a MERS-related coronavirus was recovered with additional amplicon sequencing on the MiSeq platform. The new genome shared 97.2% overall nucleotide identity to a previous Neoromicia-associated MERS-related virus, also from South Africa. Conventional PCR analysis detected diverse adenovirus and herpesvirus sequences that were widespread throughout Neoromicia populations in South Africa. Furthermore, similar adenovirus sequences were detected within these populations throughout several years. With the exception of the coronaviruses, the study represents the first report of sequence data from several viral families within a Southern African insectivorous bat genus; highlighting the need for continued investigations in this regard.
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    Carnivore conservation needs evidence based livestock protection
    (Public Library of Science, 2018-09) van Eeden, L.M.; Eklund, A.; Miller, J.R.B.; López-Bao, J.V; Chapron, G.; Cejtin, M.R.; McManus, J.
    Carnivore predation on livestock often leads people to retaliate. Persecution by humans has contributed strongly to global endangerment of carnivores. Preventing livestock losses would help to achieve three goals common to many human societies: preserve nature, protect animal welfare, and safeguard human livelihoods. Between 2016 and 2018, four independent reviews evaluated >40 years of research on lethal and nonlethal interventions for reducing predation on livestock. From 114 studies, we find a striking conclusion: scarce quantitative comparisons of interventions and scarce comparisons against experimental controls preclude strong inference about the effectiveness of methods. For wise investment of public resources in protecting livestock and carnivores, evidence of effectiveness should be a prerequisite to policy making or large-scale funding of any method or, at a minimum, should be measured during implementation. An appropriate evidence base is needed, and we recommend a coalition of scientists and managers be formed to establish and encourage use of consistent standards in future experimental evaluations.
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    Chiefs in a Democracy: A Case Study of the 'New' Systems of Regulating Firewood Harvesting in Post-Apartheid South Africa
    (MDPI, 2018-03) Findlay, S.J.; Twine, W.C.
    Much of the international commons literature reveals a decreased functioning of local traditional institutions that regulate natural resource harvesting. In South Africa, it is believed that the creation of new democratic structures at the end of Apartheid has contributed significantly to the deterioration in traditional resource regulation and this in turn has led to the extensive resource degradation seen in parts of the country. Many of these assertions, though, remain anecdotal in nature. Given the high reliance by rural households on natural resources, and the serious negative implications that over-use has on livelihood security, understanding how well or poorly such commons are regulated is key to ensuring the sustainability of such resource-dependent populations. The aim of this study was therefore to examine systems of resource governance, focusing specifically on firewood, and to determine the roles of traditional and democratically elected community leaders in six rural villages spanning two chieftaincies in Bushbuckridge, South Africa. In each study village, five local leaders were interviewed and five community focus groups were conducted. Results indicate that most parties still regard the Chief as the ultimate authority for regulating firewood harvesting. However, overall firewood management appears weak, at best, across the region. Although some authors attribute this to community confusion over the roles of local leaders in a new democracy, we provide evidence that other socio-political factors, including political expediency, may be driving the increasingly relaxed implementation of these firewood management systems. With resource dependence remaining a vital contributor to livelihood security across the developing world and with many rural communities facing increasing strain under local resource depletion, these findings shed new light on the complex social dynamics underlying the widely reported weakening of traditional institutions in South Africa. In so doing, it offers insights into local firewood governance that can be used to combat these challenges and thereby reduce regional social and ecological vulnerability being experienced in communal landscapes across the region.
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    Transplant Experiments Point to Fire Regime as Limiting Savanna Tree Distribution
    (Frontiers Media, 2018-09-18) Stevens, N.; Archibald, S.; Bond, W.J.
    Plant species range shifts are predicted to occur in response to climate change. The predictions are often based on the assumption that climate is the primary factor limiting the distribution of species. However the distribution of grassy biomes in Africa cannot be predicted by climate alone, instead interactions between vegetation, climate and disturbance structure the ecosystems. To test if climatic variables, as predicted by an environmental niche model, determine the distribution limits of two common savanna tree species we established a transplant experiment at a range of latitudes and altitudes much broader than the distribution limits of our study species. We planted seedlings of two common savanna trees, Senegalia nigrescens and Colophospermum mopane, at eight paired high and low elevation sites across an 850 km latitudinal gradient in South African savannas. At each site seedlings were planted in both grassy and cleared plots. After 2 years of growth, rainfall, temperature and location inside or outside their distribution range did not explain species success. Grass competition was the only variable that significantly affected plant growth rates across all sites, but grass competition alone could not explain the distribution limit. Species distributions were best predicted when maximum tree growth rates were considered in relation to local fire return intervals. The probability of sapling escape from the fire trap was the most likely determinant of distribution limits of these two species. As trees grew and survived 100 s of kilometers south of their current range limits we conclude that climate alone does not explain the current distribution of these trees, and that climate change adaptation strategies for savanna environments based only on climatic envelope modeling will be inappropriate.